Fixes related to polishing for release

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqsubmit/tree/master/docs/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/seqsubmit/tree/main/docs/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqsubmit/tree/master/docs/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/seqsubmit/tree/main/docs/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/seqsubmit _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).

.github/actions/nf-test/action.yml

@@ -37,7 +37,7 @@ runs:
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
+      uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')

.github/workflows/release-announcements.yml

@@ -18,7 +18,7 @@ jobs:
         id: get_description
         run: |
           echo "description=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .description')" >> $GITHUB_OUTPUT
-      - uses: rzr/fediverse-action@563159eb8d45f70ab6aaba36ed55cd037e51f441 # master
+      - uses: rzr/fediverse-action@66c2cbb5b1997666b0e28d597631b6a4f09a2719 # v0.0.6
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
           host: "mstdn.science" # custom host if not "mastodon.social" (default)

.nf-core.yml

@@ -11,12 +11,11 @@ lint:
     - docs/images/nf-core-seqsubmit_logo_light.png
     - docs/images/nf-core-seqsubmit_logo_dark.png
     - assets/nf-core-seqsubmit_logo_light.png
-    - .github/workflows/branch.yml
-    - .github/workflows/linting.yml
-nf_core_version: 4.0.2
+nf_core_version: 4.0.3
 repository_type: pipeline
 template:
-  author: Martin Beracochea, Ekaterina Sakharova, Sofia Ochkalova, Evangelos Karatzas, Tim Rozday
+  author: Martin Beracochea, Ekaterina Sakharova, Sofia Ochkalova, Evangelos Karatzas,
+    Tim Rozday
   description: Submit sequences, assemblies, MAGs, etc., to public archives
   force: false
   is_nfcore: true

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0.0 - [date]
+## v1.0.0 - 01/08/2026
 
 Initial release of nf-core/seqsubmit, created with the [nf-core](https://nf-co.re/) template.
 

assets/schema_input_assembly.json

@@ -7,10 +7,11 @@
     "items": {
         "type": "object",
         "properties": {
-            "sample": {
+            "id": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample must be provided and cannot contain spaces",
+                "description": "A unique identifier for this data entry. Must be globally unique within the input dataset",
+                "errorMessage": "ID must be provided and cannot contain spaces",
                 "meta": ["id"]
             },
             "fasta": {
@@ -19,7 +20,7 @@
                 "exists": true,
                 "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.(fa|fasta|fna)\\.gz$",
                 "errorMessage": "FASTA file must be provided and have extension '.fa.gz', '.fasta.gz', '.fna.gz'",
-                "description": "Metagenomic assembly FASTA file"
+                "description": "Path to assembly contigs in FASTA format compressed with gzip"
             },
             "fastq_1": {
                 "anyOf": [
@@ -34,8 +35,9 @@
                         "maxLength": 0
                     }
                 ],
+                "default": null,
                 "errorMessage": "FASTQ file must have extension '.fq' or '.fastq' (optionally gzipped)",
-                "description": "Forward reads if paired-end or single-end reads FASTQ file"
+                "description": "Path to single-end/paired-end forward reads in FASTQ format (optionally gzipped). Required if coverage is not provided"
             },
             "fastq_2": {
                 "anyOf": [
@@ -50,43 +52,49 @@
                         "maxLength": 0
                     }
                 ],
+                "default": null,
                 "errorMessage": "FASTQ file for reverse reads must have extension '.fq' or '.fastq' (optionally gzipped)",
-                "description": "Reverse reads FASTQ file if paired-end. Leave empty for single-end reads"
+                "description": "Path to reverse reads in FASTQ format for paired-end data (optionally gzipped). Leave empty for single-end reads"
             },
             "coverage": {
                 "anyOf": [
                     {
                         "type": "number",
-                        "minimum": 0
+                        "exclusiveMinimum": 0
                     },
                     {
                         "type": "string",
                         "maxLength": 0
                     }
                 ],
+                "default": null,
                 "errorMessage": "Coverage must be a positive number or empty",
-                "description": "Estimated value of assembly coverage"
+                "description": "Estimated sequencing depth of the assembly (optional). If this value is missing, it is computed automatically during pipeline execution when reads are provided",
+                "meta": ["coverage"]
             },
             "run_accession": {
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Accession must be provided and cannot contain spaces",
-                "description": "Accession of the run used to generate the assembly"
+                "description": "ENA run accession for the reads used to generate the metagenomic assembly. Reads must already be submitted to ENA",
+                "meta": ["run_accession"]
             },
             "assembler": {
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Assembler must be provided and cannot contain spaces",
-                "description": "Name of the assembler software used to generate the assembly"
+                "description": "Name of the assembler software used to generate the assembly, e.g. MEGAHIT, SPAdes, metaSPAdes, Flye, etc",
+                "meta": ["assembler"]
             },
             "assembler_version": {
                 "anyOf": [{ "type": "string" }, { "type": "number" }],
                 "pattern": "^\\S+$",
                 "errorMessage": "Assembler version must be provided and cannot contain spaces",
-                "description": "Version of the assembler software used to generate the assembly"
+                "description": "Version of the assembler software used to generate the assembly, e.g. 1.0.0",
+                "meta": ["assembler_version"]
             }
         },
-        "required": ["sample", "fasta", "run_accession", "assembler", "assembler_version"],
+        "required": ["id", "fasta", "run_accession", "assembler", "assembler_version"],
         "anyOf": [
             {
                 "properties": {
@@ -101,7 +109,7 @@
                 "properties": {
                     "coverage": {
                         "type": "number",
-                        "minimum": 0
+                        "exclusiveMinimum": 0
                     }
                 },
                 "required": ["coverage"]

assets/schema_input_genome.json

@@ -7,23 +7,25 @@
     "items": {
         "type": "object",
         "properties": {
-            "sample": {
+            "id": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "description": "A unique identifier for this data entry. Must be globally unique within the input dataset",
+                "errorMessage": "ID must be provided and cannot contain spaces",
                 "meta": ["id"]
             },
             "fasta": {
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
                 "pattern": "^([\\S\\s]*\\/)?[^\\s\\/]+\\.(fa|fasta|fna)\\.gz$",
-                "errorMessage": "FASTA file for sequences 1 must be provided, cannot contain spaces and must have extension '.fa.gz', '.fasta.gz', or '.fna.gz'",
-                "description": "MAG/bin sequence file"
+                "errorMessage": "Path to the FASTA file must be provided, cannot contain spaces and must have extension '.fa.gz', '.fasta.gz', or '.fna.gz'",
+                "description": "Path to MAG/bin sequences in FASTA format compressed with `gzip`. All names of the FASTA files must be unique to prevent pipeline errors. File should contain at least one sequence"
             },
             "accession": {
                 "type": "string",
-                "description": "Run or assembly ENA accession"
+                "description": "ENA accession of the run or metagenomic assembly used to generate the MAG/bin. Reads or assembly must already be submitted to ENA",
+                "meta": ["accession"]
             },
             "fastq_1": {
                 "anyOf": [
@@ -38,8 +40,9 @@
                         "maxLength": 0
                     }
                 ],
+                "default": null,
                 "errorMessage": "FASTQ file must have extension '.fq' or '.fastq' (optionally gzipped)",
-                "description": "Forward reads if paired-end or single-end reads FASTQ file"
+                "description": "Path to single-end/paired-end forward reads (in FASTQ format, optionally gzipped) used to generate the source metagenomic assembly. Required if genome_coverage is not provided"
             },
             "fastq_2": {
                 "anyOf": [
@@ -54,68 +57,126 @@
                         "maxLength": 0
                     }
                 ],
+                "default": null,
                 "errorMessage": "FASTQ file for reverse reads must have extension '.fq' or '.fastq' (optionally gzipped)",
-                "description": "Reverse reads FASTQ file if paired-end. Leave empty for single-end reads"
+                "description": "Path to reverse reads in FASTQ format for paired-end data (optionally gzipped) used to generate the source metagenomic assembly. Leave empty for single-end reads"
             },
             "assembly_software": {
                 "type": "string",
-                "description": "Tool name and version that was used to assemble data"
+                "description": "Tool name and version that was used to assemble data, e.g. MEGAHIT_v1.0, SPAdes_v4.0.0, metaSPAdes_v3.15.0",
+                "meta": ["assembly_software"]
             },
             "binning_software": {
                 "type": "string",
-                "description": "Tool name and version that was used to bin data"
+                "description": "Tool name and version that was used to bin data, e.g. MetaBAT2_v1.0, VAMB_2.0, MaxBin2_v1, CONCOCT_v3.0, SemiBin2_v1, COMEBin_v2.3.4, etc",
+                "meta": ["binning_software"]
             },
             "binning_parameters": {
                 "type": "string",
-                "description": "Arguments used to bin data different from default"
+                "description": "Arguments used to bin data different from default, e.g. -min_contig_length 1000, otherwise use 'default'",
+                "meta": ["binning_parameters"]
             },
             "stats_generation_software": {
                 "type": "string",
-                "description": "Tool(s) used to estimate completeness and contamination"
+                "default": null,
+                "description": "Tool, including version, that was used to calculate completeness and contamination, e.g. CheckM2_v1.0.0",
+                "meta": ["stats_generation_software"]
             },
             "completeness": {
-                "type": "number",
-                "description": "MAG/bin completeness value"
+                "anyOf": [
+                    {
+                        "type": "number",
+                        "minimum": 0,
+                        "maximum": 100
+                    },
+                    {
+                        "type": "string",
+                        "maxLength": 0
+                    }
+                ],
+                "default": null,
+                "description": "MAG/bin completeness score: the 0<= ratio <= 100 of observed single-copy marker genes to total single-copy marker genes in chosen marker gene set (%). ENA docs: https://ena-docs.readthedocs.io/en/latest/faq/metagenomes.html#how-is-the-quality-of-a-metagenomic-assembly-defined",
+                "meta": ["completeness"]
             },
             "contamination": {
-                "type": "number",
-                "description": "MAG/bin contamination value"
+                "anyOf": [
+                    {
+                        "type": "number",
+                        "minimum": 0,
+                        "maximum": 100
+                    },
+                    {
+                        "type": "string",
+                        "maxLength": 0
+                    }
+                ],
+                "default": null,
+                "description": "MAG/bin contamination score: the 0<= ratio <= 100 of observed single-copy marker genes in ≥2 copies to total single-copy marker genes in chosen marker gene set (%). ENA docs: https://ena-docs.readthedocs.io/en/latest/faq/metagenomes.html#how-is-the-quality-of-a-metagenomic-assembly-defined",
+                "meta": ["contamination"]
             },
             "genome_coverage": {
-                "type": "number",
-                "description": "MAG/bin coverage value"
+                "anyOf": [
+                    {
+                        "type": "number",
+                        "exclusiveMinimum": 0
+                    },
+                    {
+                        "type": "string",
+                        "maxLength": 0
+                    }
+                ],
+                "default": null,
+                "description": "Estimated average sequencing depth (>0) across the genome. If the value is missing, it is computed automatically during pipeline execution when reads are provided",
+                "meta": ["genome_coverage"]
             },
             "metagenome": {
                 "type": "string",
-                "description": "ENA accepted metagenome name"
+                "description": "Registered metagenome taxonomic identifier or name that matches an existing ENA taxonomy entry. It needs to be listed in the taxonomy tree https://www.ebi.ac.uk/ena/browser/view/408169?show=tax-tree (you might need to press \"Tax tree - Show\" in the right most section of the page). Full list can also be found https://github.com/EBI-Metagenomics/genome_uploader/blob/main/genomeuploader/constants.py#L22",
+                "meta": ["metagenome"]
             },
             "co-assembly": {
-                "type": "string",
-                "description": "Yes if data was co-assembled, No otherwise"
+                "type": "boolean",
+                "description": "Whether a co-assembly strategy was used for the initial metagenomic assembly generation. Options: 'true' or 'false'",
+                "meta": ["co_assembly"]
             },
             "broad_environment": {
                 "type": "string",
-                "description": "broad ecological context of a sample"
+                "description": "Broad ecological context of the sample, for example 'marine biome', 'desert biome'. It is recommended to use subclasses of EnvO 'biome' class (http://purl.obolibrary.org/obo/ENVO_00000428). Documentation: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS",
+                "meta": ["broad_environment"]
             },
             "local_environment": {
                 "type": "string",
-                "description": "local ecological context"
+                "description": "Local environmental context of the sample, for example 'tropical dry broadleaf forest biome', 'marine abyssal zone biome'. It is recommended to use EnvO terms which are of smaller spatial grain than your entry for \"broad-scale environmental context\". Documentation: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS",
+                "meta": ["local_environment"]
             },
             "environmental_medium": {
                 "type": "string",
-                "description": "material displaced by the sample"
+                "description": "Material surrounding and in contact with the sample, for example 'mucus', 'lake water'. It is recommended to use subclasses of EnvO 'environmental material' class (http://purl.obolibrary.org/obo/ENVO_00010483). Documentation: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS",
+                "meta": ["environmental_medium"]
             },
             "RNA_presence": {
-                "type": "string",
-                "description": "Yes/No if at least 18 tRNAs and 5S, 16S, 23S rRNA genes detected"
+                "anyOf": [
+                    {
+                        "type": "boolean"
+                    },
+                    {
+                        "type": "string",
+                        "maxLength": 0
+                    }
+                ],
+                "default": null,
+                "description": "Presence or absence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs. This is used for MISAG/MIMAG assembly quality classification. Options: 'true' or 'false'",
+                "meta": ["RNA_presence"]
             },
             "NCBI_lineage": {
                 "type": "string",
-                "description": "full NCBI lineage - format: x;y;z"
+                "default": null,
+                "description": "Full NCBI lineage - format: x;y;z. For example, the lineage for E. coli can be: 'Bacteria;Pseudomonadati;Pseudomonadota;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Escherichia' or '2;1224;1236;91347;543;561;562'. For more info check https://www.ncbi.nlm.nih.gov/datasets/docs/v2/data-processing/taxonomy-processing/taxonomy/",
+                "meta": ["NCBI_lineage"]
             }
         },
         "required": [
-            "sample",
+            "id",
             "fasta",
             "accession",
             "assembly_software",
@@ -141,7 +202,7 @@
                 "properties": {
                     "genome_coverage": {
                         "type": "number",
-                        "minimum": 0
+                        "exclusiveMinimum": 0
                     }
                 },
                 "required": ["genome_coverage"]